Nine months ago, scenes of 1,700 captured soldiers being marched through the streets of Tikrit became a defining emblem of the Isis takeover of northern Iraq. On Tuesday, the whereabouts of the hundreds of men who had been missing ever since finally became clear as rescuers began excavating eight mass graves, not far from where the soldiers were captured.

The burial sites appear to confirm fears that all of those still missing have been killed. The atrocity is thought to be one of the worst of its kind since Isis forces began their rampage, vowing to destroy Baghdad’s Shia-led government.

The few soldiers who managed to escape during the carnage in Iraq’s fourth city had spoken at the time of Shia soldiers being separated from Sunnis and the latter being freed. The Shias among them were shown no mercy and their ordeal became a rallying call in the battle to take back Tikrit, which was led by a group of Shia militias, along with the Iraqi military, and ended this week with Isis suffering its most significant defeat yet.

Forensic specialists arrived early on Tuesday at the sites near the Camp Speicher military base from where the men were seized in early June 2014. Until Tikrit was declared retaken late last week, the location of the graves had been widely known, but only two of them were in areas not controlled by the terror group.

The Guardian visited one mass grave on a barren hilltop overlooking the east of the now ravaged city in late March. The stench of death wafted from the hard-packed soil and a militia checkpoint on a nearby road regularly moved to avoid winds turning the fumes their way.

Around 40 soldiers were thought to have been dumped there. Scores more were dumped in each of the other six to eight sites that have now been partially excavated. Some of the diggers were colleagues of the missing men, while others were family members. There were reports of soldiers and relatives collapsing after believing they had recognised their dead colleagues or kin.

Isis had brutally publicised the deaths of some of the men, whom they forced to lie in the dirt before killing them, expecting the gruesome scenes to spark fear among communities they were trying to conquer. Some bodies were dumped in the nearby Tigris river and others left to rot. But as yet, the full tally of the missing remains unaccounted for.

 “The families of the victims were thankful and they visited these mass graves,” said Naim al-Ubaidi, a spokesman for Asa’ib Ahl al-Haq, one of the most powerful of the Shia militias involved in the fighting for Tikrit under the banner of Hashd al-Shaabi. “Most of them are grateful that now they can now bury their sons and close that chapter of their lives. People were living in agony not knowing the future of their sons and now they know they are going to rest in peace.”

A sweep of Tikrit, much of which now lies in ruins, has revealed no prison sites and Iraqi officials believe that none of the missing remain alive.

“So far we have found six to eight mass graves and we don’t have the number of victims yet,” said Ubaidi. “We will use DNA to establish the true number.

“We managed to find these mass graves with the help of locals from the area who told us where the killings happened. They also brought us some of the ID cards that fell from these soldiers as they were being dragged away. The majority of the deaths were caused by shots to the head.”

 

The fall of Tikrit has given Baghdad the chance to boast it is rolling back Isis forces which were only 20 miles from the capital’s western outskirts last August. All along the highway from Baghdad to Tikrit, there is evidence of where the terror group was until the concerted campaign to fight it began in earnest in late February

hile the gains are undeniable – up to 7,000 sq km (2,700 sq miles) has now been cleared, according to Hashd al-Shaabi’s leader, Haidar al-Ameri – the dominant military power has often been the militia groups. Iraq’s army, which fled northern Iraq last summer as Isis advanced, has partially regrouped, and played a prominent role in the final battle for Tikrit. However, doubts endure about whether it can take primacy over the militia groups, critics of which say are more loyal to their sect than the state.

Hashd al-Shaabi and Iraqi officials have been at pains to say the war is not being fought against Iraq’s Sunnis. However Sunni communities have been transformed into wastelands by the fighting, with militias responsible for at least some of the destruction and subsequent looting.

Nevertheless, there is evidence of a growing number of Sunni tribes allying with the Shia forces and national army – a move that all sides deem to be essential before an expected summer push to take back Mosul.

“The tribes enrolled with us and fought Isis,” said Ubaidi, whose militia played a prominent role in Iraq’s civil war. “I’m sure the same will apply to Mosul. People in Mosul are quiet now because they are afraid from Isis but once they know such a force is coming, they will join them and fight the terrorists.”

Meanwhile, Isis militants were holding firm in the Yarmouk Palestinian refugee camp in Damascus, four days after they stormed the area claiming to free its remaining residents from a brutal two-year siege.

The UN demanded urgent access to the camp, which is close to the heart of the Syrian capital. Syrian officials suggested that trapped residents would be allowed to leave – something that many had been prevented from doing throughout the blockade.